Ecological networks balance connectivity with flexibility to perturbations

This archive contains the data and computational materials associated with the manuscript Ecological networks balance connectivity with flexibility to perturbations, by Giménez-Romero et al. The study analyses ecological interaction networks from the Web of Life and Mangal databases to examine how connectance, interaction richness, and thermodynamic network efficiency scale with species richness across interaction types. The archive includes the original ecological-network data obtained from Web of Life and Mangal, processed ecological networks, structural network metrics, precomputed outputs from the null-model and perturbation analyses, and the code and notebooks used to perform the analyses and generate the figures. The initial collection comprised 1,801 ecological interaction networks. After applying the preprocessing criteria, 1,569 networks remained, of which 36 duplicates shared between the source databases were removed. The final analytical dataset therefore contains 1,533 ecological interaction networks. Thermodynamic-efficiency analyses were performed on a subset of 1,268 networks with more than five species. The archive retains the original and processed network collections, including networks excluded from the final analyses. Networks are stored in GraphML format and include metadata such as source database, interaction type, and network identifier. The file Results/field_studies_metrics_network.csv contains structural descriptors, including species richness, number of interactions, connectance, mean degree, and other network properties. The filtering and deduplication procedures used to obtain the final analytical datasets are implemented in the accompanying notebooks. The Python code implements the computation of thermodynamic efficiency across propagation scales, Erdős–Rényi null models, configuration-model null models, Curveball fixed-marginal null models for bipartite graphs, and link-addition/link-removal perturbation analyses. The archive also includes notebooks for processing the network data, performing the statistical analyses, and generating the manuscript and Supplementary Information figures. The analysis code is also maintained in the GitHub repository. The original ecological interaction networks are available from the Web of Life and Mangal databases. This Zenodo archive provides the processed data, derived metrics, computational outputs, and analysis materials associated with the revised manuscript, allowing the reported results to be independently examined and reproduced.